Not sure if it counts but I own physical and digital copies of Xenoblade 2, Octopath Traveler and Pikmin 3.

I have every Zelda game on everything it ever came out on, physically at least, an besides that not so much, except if you’re going to count remasters.

I own Call of Duty Infinity Warfare twice on Xbox One.

I bought the CoD IW Legacy edition (with CoD4 Remastered) from Italian Amazon. I played CoD 4 Remastered first and CoD IW a few weeks later. After installing it I noticed that the game was indeed in Italian even though my Xbox was set to English. It turned out the game didn't have any English dub on the disc. Only languages available were Italian and Spanish.
This is VERY unusual for 8th gen games. I bought lots of games from Italy and France and they all came with at least English (aka the standard dub language) but Activision doesn't care and releases their CoD games without an English track in those countries.
Anyway I couldn't send it back anymore so I bought Infinite Warfare once more to be able to play it in English.

Oh, I just realized. I have two copies of Pikmin 3 for Wii U, one unopened and the other used. 

ICO PS2 PAL version, PS2 US version, PS3 remaster
SotC, PS2 US version, PS3 remaster, PS4 remake
Ratchet and Clank series, PS2, PS3 remasters
Jak and Daxter series, PS2, PS3 remasters, PSP spin off.
Burnout 3 Takedown, PS2, XBox 360
Okami, PS2, PS4 remaster
Grim Fandango, physical PC edition, PS4 remaster
Zelda Windwaker, GC, WiiU remake
TLoU, PS3 version, PS4 remaster
Journey/Flower/Flow, digital PS3 and physical PS4 edition
GT Sport, steelbook physical edition, digital edition
No Man's sky, physical and digital edition.
DriveClub, physical edition and PSVR edition
Skyrim, PS3 and PSVR
Fez 360, PS4

Princess Mononoke wins though,
2 DVD editions, Hong Kong intl Blu-ray, Disney Blu-ray, Ghibli Steelbook edition

Minecraft comes close thanks to my kids, PC (x2), PS4, iPad and Dungeons on Switch

I own multiple copies of Submarine Titans on PC. They're the same edition, though.

I have Hollow Knight for both the Switch and the PS4, because its the best Metroidvania of the last 15 years and I wanted to play it on the go and platinum it.

I never bought a game on console and PC. I have rebought old game on GOG and Steam that I had previously bought a box copy for before digital games was a thing.

Games that come to mind
Quest of Glories series
Diablo 1/2
Neverwinter Night
A lot of the old D&D gold box games
Older elder scroll games
Master of Magic

and am sure I forgetting a few

Let's see, I bought

• Brütal Legend on the Xbox360 and the on PC (Steam, through a Humble Bundle)
• Mass Effect on Xbox360 and for PC (Steam)
• Metroid Prime 1&2 on the GameCube and then again for the Wii
• SimCity 4 physical and then digital, Steam

Those are the ones I can think of that I bought twice.

Then there are those games that were offered for free that I claimed again. There are too many of those to list them all, but they are the bulk of my GOG library thanks to GOG Connect.

I think I still have two Super Mario World cartridges. One that came with my Super Nintendo, and a second one that my late grandmother gave me as a gift. After she passed away, I keep it as a memento.